After upgrading our JIRA from 4.1.2, to 4.4, and eventually up to 5.0.2, some of our projects cannot view their Source within their Project page within JIRA and receive the error from the Question above. Other projects can see their source though.
It would appear that our application authentications were not working correctly even though they were done using the Atlassian guidelines. Once we figured this out and change the authentication type, we were able to setup the project links and this was resolved.
We had problems actually modifying the existing Application Link, so we removed the existing on and created a new one. Within the new App Link, set your information to the following:
Application Name: <server short name> (i.e., my-fisheye) without domain suffix
Application URL: <URL and port> (i.e., http://my-fisheye.domain:8060) don't use the /browse suffix
Display URL: Same as Application URL
Outgoing Authenication: Basic Access
Incoming Authentication: Trusted Authentication
Once you have your authentication squared away, you have to go into each project > Summary>Settings and Configure Project Links.
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